The 1999–2000 season was Ionikos' 6th straight season on the Greek first tier and the 9th season on that tier overall. Managing a lower league finish than the previous season, their biggest feat was reaching the domestic cup final.
Source: Galanis Sports Data Rules for classification: 1) Points; 2) Head-to-head points; 3) Head-to-head goal difference; 4) Goal difference; 5) Goals scored; 6) Goals against; 7) Play-offs (neutral ground); 8) Draw. (Note: Criterion 7 is only used if needed to decide champion, teams for relegation or teams for UEFA competitions). Notes: